Substantial effort and funding are currently being expended in the genomics and proteomics fields with the focus of much of this effort being the discovery of new therapeutic and diagnostic agents. These therapeutic and diagnostic agents may work at the DNA (or RNA) level, the field of genomics, or at the protein level, the field of proteomics. In either case, the activity of a therapeutic and/or diagnostic agent resides in the ability of the drug molecule to bind tightly to a specific target molecule and through this complex formation to alter the function of the target molecule.
Currently there are two prevailing approaches to evaluate how effectively a particular drug binds with a target molecule, such as a nucleic acid or protein: the structural approach and the functional approach. The structural approach is based on predicting the potential of binding interactions from knowledge of the 3-D structures of the interacting molecules. This geometric approach, which evaluates how well the target molecule and drug molecule might fit together, is used to minimize the number of potential drug molecules that should be studied in detail. The functional approach is based on measurement of the change in the biological function of a nucleic acid or protein in the presence of the therapeutic agent.